Of course! No matter which helpdesk you use, you can create tags for each selling channel from inside your ChannelReply account. See "Creating and Using ChannelReply Tags."
Every eBay, Etsy, Back Market, Newegg, Shopify or Walmart account you connect can have its own unique tag. This tag will appear on every message from that particular selling account.
For Amazon, we get even more granular, and you can create a separate tag for each Amazon marketplace and/or brand you connect. For example, you could have different tags for Amazon Brand 1 in the US, Amazon Brand 1 in Canada, and Amazon Brand 2 in the US.